AMR++ Bioinformatic pipeline

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        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        About MultiQC

        This report was generated using MultiQC, version 1.13

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/ewels/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        AMR++ Bioinformatic pipeline
        A pipeline meant to aid in the analysis of raw sequencing reads to characterize the profile of antimicrobial resistance genes, or resistome.

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Contact E-mail
        meglab.metagenomics@gmail.com
        Application Type
        AMR++
        Project Type
        FastQC analysis

        Report generated on 2022-11-30, 20:55 MST based on data in: /s/angus/h/nobackup/work/87/3c56c3ee9c0588a2251119efcb4780


        General Statistics

        Showing 292/292 rows and 4/6 columns.
        Sample Name# Variants% Dups% GCM Seqs
        PT010D1T0_GuelphTEAMR_S3_L001_R1_001
        76.0%
        48%
        42.6
        PT010D1T0_GuelphTEAMR_S3_L001_R2_001
        72.7%
        48%
        42.6
        PT010H1T0_GuelphTEAMR_S1_L001_R1_001
        71.3%
        49%
        45.1
        PT010H1T0_GuelphTEAMR_S1_L001_R2_001
        66.2%
        49%
        45.1
        PT010H2T0_GuelphTEAMR_S2_L001_R1_001
        72.9%
        51%
        36.7
        PT010H2T0_GuelphTEAMR_S2_L001_R2_001
        68.2%
        51%
        36.7
        PT012D1T0_GuelphTEAMR_S5_L001_R1_001
        26.7%
        42%
        52.1
        PT012D1T0_GuelphTEAMR_S5_L001_R2_001
        24.8%
        42%
        52.1
        PT012H1T0_GuelphTEAMR_S4_L001_R1_001
        64.6%
        52%
        34.1
        PT012H1T0_GuelphTEAMR_S4_L001_R2_001
        60.0%
        52%
        34.1
        PT014D1T0_GuelphTEAMR_S7_L001_R1_001
        24.0%
        42%
        95.3
        PT014D1T0_GuelphTEAMR_S7_L001_R2_001
        23.9%
        42%
        95.3
        PT014H1T0_GuelphTEAMR_S6_L001_R1_001
        22.8%
        48%
        9.6
        PT014H1T0_GuelphTEAMR_S6_L001_R2_001
        21.8%
        48%
        9.6
        PT015D1T0_GuelphTEAMR_S12_L001_R1_001
        67.5%
        50%
        37.7
        PT015D1T0_GuelphTEAMR_S12_L001_R2_001
        63.5%
        50%
        37.7
        PT015H1T0_GuelphTEAMR_S8_L001_R1_001
        32.9%
        50%
        17.4
        PT015H1T0_GuelphTEAMR_S8_L001_R2_001
        31.9%
        50%
        17.4
        PT015H2T0_GuelphTEAMR_S9_L001_R1_001
        72.8%
        53%
        38.4
        PT015H2T0_GuelphTEAMR_S9_L001_R2_001
        68.6%
        53%
        38.4
        PT015H3T0_GuelphTEAMR_S10_L001_R1_001
        79.9%
        51%
        32.6
        PT015H3T0_GuelphTEAMR_S10_L001_R2_001
        77.5%
        51%
        32.6
        PT015H4T0_GuelphTEAMR_S11_L001_R1_001
        80.9%
        51%
        34.2
        PT015H4T0_GuelphTEAMR_S11_L001_R2_001
        76.8%
        51%
        34.2
        PT017D1T0_GuelphTEAMR_S14_L001_R1_001
        68.9%
        48%
        27.8
        PT017D1T0_GuelphTEAMR_S14_L001_R2_001
        65.4%
        48%
        27.8
        PT017H1T0_GuelphTEAMR_S13_L001_R1_001
        71.1%
        52%
        36.3
        PT017H1T0_GuelphTEAMR_S13_L001_R2_001
        67.7%
        52%
        36.3
        PT019D1T0B_GuelphTEAMR_S70_L002_R1_001
        69.9%
        51%
        18.4
        PT019D1T0B_GuelphTEAMR_S70_L002_R2_001
        67.7%
        51%
        18.4
        PT019D1T0_GuelphTEAMR_S17_L001_R1_001
        73.9%
        51%
        24.4
        PT019D1T0_GuelphTEAMR_S17_L001_R2_001
        70.4%
        51%
        24.4
        PT019H1T0_GuelphTEAMR_S15_L001_R1_001
        72.4%
        51%
        29.8
        PT019H1T0_GuelphTEAMR_S15_L001_R2_001
        67.9%
        51%
        29.8
        PT019H2T0_GuelphTEAMR_S16_L001_R1_001
        79.7%
        51%
        40.6
        PT019H2T0_GuelphTEAMR_S16_L001_R2_001
        77.3%
        51%
        40.6
        PT021D1T0_GuelphTEAMR_S19_L001_R1_001
        69.7%
        49%
        29.4
        PT021D1T0_GuelphTEAMR_S19_L001_R2_001
        66.4%
        49%
        29.4
        PT021D2T0_GuelphTEAMR_S20_L001_R1_001
        74.9%
        49%
        26.0
        PT021D2T0_GuelphTEAMR_S20_L001_R2_001
        68.8%
        49%
        26.0
        PT021H2T0_GuelphTEAMR_S18_L001_R1_001
        68.6%
        48%
        27.6
        PT021H2T0_GuelphTEAMR_S18_L001_R2_001
        66.8%
        48%
        27.6
        PT023D1T0_GuelphTEAMR_S23_L001_R1_001
        61.6%
        50%
        26.1
        PT023D1T0_GuelphTEAMR_S23_L001_R2_001
        58.2%
        50%
        26.1
        PT023H1T0_GuelphTEAMR_S21_L001_R1_001
        66.1%
        51%
        48.0
        PT023H1T0_GuelphTEAMR_S21_L001_R2_001
        62.6%
        51%
        48.0
        PT023H2T0_GuelphTEAMR_S22_L001_R1_001
        63.0%
        51%
        32.1
        PT023H2T0_GuelphTEAMR_S22_L001_R2_001
        59.0%
        51%
        32.1
        PT024D1T0B_GuelphTEAMR_S71_L002_R1_001
        72.9%
        49%
        34.0
        PT024D1T0B_GuelphTEAMR_S71_L002_R2_001
        71.8%
        49%
        34.0
        PT024D1T0_GuelphTEAMR_S26_L001_R1_001
        66.5%
        50%
        21.7
        PT024D1T0_GuelphTEAMR_S26_L001_R2_001
        63.6%
        50%
        21.7
        PT024H1T0_GuelphTEAMR_S24_L001_R1_001
        57.6%
        51%
        22.2
        PT024H1T0_GuelphTEAMR_S24_L001_R2_001
        54.7%
        51%
        22.2
        PT024H2T0_GuelphTEAMR_S25_L001_R1_001
        79.4%
        52%
        31.2
        PT024H2T0_GuelphTEAMR_S25_L001_R2_001
        74.4%
        52%
        31.2
        PT026D1T0_GuelphTEAMR_S28_L001_R1_001
        62.9%
        47%
        38.6
        PT026D1T0_GuelphTEAMR_S28_L001_R2_001
        56.7%
        47%
        38.6
        PT026H1T0_GuelphTEAMR_S27_L001_R1_001
        68.3%
        51%
        31.2
        PT026H1T0_GuelphTEAMR_S27_L001_R2_001
        64.7%
        51%
        31.2
        PT046D1T0B_GuelphTEAMR_S72_L002_R1_001
        79.2%
        48%
        44.9
        PT046D1T0B_GuelphTEAMR_S72_L002_R2_001
        78.0%
        48%
        44.9
        PT046D1T0_GuelphTEAMR_S30_L001_R1_001
        84.9%
        49%
        84.6
        PT046D1T0_GuelphTEAMR_S30_L001_R2_001
        80.6%
        49%
        84.6
        PT046H1T0_GuelphTEAMR_S29_L001_R1_001
        59.5%
        50%
        31.6
        PT046H1T0_GuelphTEAMR_S29_L001_R2_001
        55.6%
        50%
        31.6
        PT050D1T0B_GuelphTEAMR_S73_L002_R1_001
        69.5%
        48%
        32.2
        PT050D1T0B_GuelphTEAMR_S73_L002_R2_001
        68.3%
        48%
        32.2
        PT050D1T0_GuelphTEAMR_S32_L001_R1_001
        75.9%
        49%
        36.6
        PT050D1T0_GuelphTEAMR_S32_L001_R2_001
        73.5%
        49%
        36.6
        PT050H1T0_GuelphTEAMR_S31_L001_R1_001
        70.2%
        50%
        25.8
        PT050H1T0_GuelphTEAMR_S31_L001_R2_001
        68.1%
        50%
        25.8
        PT051D1T0_GuelphTEAMR_S35_L001_R1_001
        75.3%
        49%
        32.5
        PT051D1T0_GuelphTEAMR_S35_L001_R2_001
        72.0%
        49%
        32.5
        PT051D2T0_GuelphTEAMR_S36_L001_R1_001
        68.4%
        48%
        29.3
        PT051D2T0_GuelphTEAMR_S36_L001_R2_001
        64.3%
        48%
        29.3
        PT051D3T0_GuelphTEAMR_S37_L001_R1_001
        73.7%
        48%
        28.3
        PT051D3T0_GuelphTEAMR_S37_L001_R2_001
        70.4%
        48%
        28.3
        PT051D5T0_GuelphTEAMR_S38_L001_R1_001
        80.5%
        47%
        38.3
        PT051D5T0_GuelphTEAMR_S38_L001_R2_001
        76.6%
        47%
        38.3
        PT051H1T0_GuelphTEAMR_S33_L001_R1_001
        79.0%
        50%
        37.1
        PT051H1T0_GuelphTEAMR_S33_L001_R2_001
        75.9%
        50%
        37.1
        PT051H2T0_GuelphTEAMR_S34_L001_R1_001
        65.2%
        51%
        27.3
        PT051H2T0_GuelphTEAMR_S34_L001_R2_001
        60.9%
        51%
        27.3
        PT052D1T0_GuelphTEAMR_S40_L001_R1_001
        68.2%
        51%
        30.7
        PT052D1T0_GuelphTEAMR_S40_L001_R2_001
        65.0%
        51%
        30.7
        PT052H1T0_GuelphTEAMR_S39_L001_R1_001
        74.9%
        53%
        30.5
        PT052H1T0_GuelphTEAMR_S39_L001_R2_001
        72.1%
        53%
        30.5
        PT053D1T0_GuelphTEAMR_S42_L001_R1_001
        78.4%
        49%
        36.3
        PT053D1T0_GuelphTEAMR_S42_L001_R2_001
        75.4%
        49%
        36.3
        PT053H1T0_GuelphTEAMR_S41_L001_R1_001
        65.8%
        49%
        20.5
        PT053H1T0_GuelphTEAMR_S41_L001_R2_001
        62.1%
        49%
        20.5
        PT054D1T0_GuelphTEAMR_S44_L001_R1_001
        73.7%
        50%
        48.3
        PT054D1T0_GuelphTEAMR_S44_L001_R2_001
        68.7%
        50%
        48.3
        PT054H1T0_GuelphTEAMR_S43_L001_R1_001
        48.4%
        52%
        29.9
        PT054H1T0_GuelphTEAMR_S43_L001_R2_001
        45.6%
        52%
        29.9
        PT114D1T0_GuelphTEAMR_S24_L002_R1_001
        6.1%
        44%
        35.0
        PT114D1T0_GuelphTEAMR_S24_L002_R2_001
        6.1%
        44%
        35.0
        PT114D1T1_GuelphTEAMR_S27_L002_R1_001
        75.6%
        48%
        34.3
        PT114D1T1_GuelphTEAMR_S27_L002_R2_001
        74.6%
        48%
        34.3
        PT114H1T0_GuelphTEAMR_S22_L002_R1_001
        51.9%
        49%
        30.6
        PT114H1T0_GuelphTEAMR_S22_L002_R2_001
        49.8%
        49%
        30.6
        PT114H1T1_GuelphTEAMR_S25_L002_R1_001
        39.0%
        48%
        31.4
        PT114H1T1_GuelphTEAMR_S25_L002_R2_001
        37.8%
        48%
        31.4
        PT114H2T0_GuelphTEAMR_S23_L002_R1_001
        5.5%
        45%
        28.1
        PT114H2T0_GuelphTEAMR_S23_L002_R2_001
        5.4%
        45%
        28.1
        PT114H2T1_GuelphTEAMR_S26_L002_R1_001
        42.9%
        51%
        30.3
        PT114H2T1_GuelphTEAMR_S26_L002_R2_001
        40.8%
        51%
        30.3
        PT118D1T0_GuelphTEAMR_S29_L002_R1_001
        74.1%
        46%
        43.6
        PT118D1T0_GuelphTEAMR_S29_L002_R2_001
        72.8%
        46%
        43.6
        PT118D1T1_GuelphTEAMR_S31_L002_R1_001
        67.1%
        47%
        22.0
        PT118D1T1_GuelphTEAMR_S31_L002_R2_001
        64.2%
        47%
        22.0
        PT118H1T0_GuelphTEAMR_S28_L002_R1_001
        72.0%
        48%
        30.5
        PT118H1T0_GuelphTEAMR_S28_L002_R2_001
        69.7%
        48%
        30.5
        PT118H1T1_GuelphTEAMR_S30_L002_R1_001
        68.4%
        49%
        25.7
        PT118H1T1_GuelphTEAMR_S30_L002_R2_001
        67.0%
        49%
        25.7
        PT120D1T0_GuelphTEAMR_S34_L002_R1_001
        32.9%
        51%
        20.8
        PT120D1T0_GuelphTEAMR_S34_L002_R2_001
        31.9%
        51%
        20.8
        PT120D1T1_GuelphTEAMR_S39_L002_R1_001
        68.2%
        49%
        35.0
        PT120D1T1_GuelphTEAMR_S39_L002_R2_001
        66.3%
        49%
        35.0
        PT120D2T0_GuelphTEAMR_S35_L002_R1_001
        50.8%
        51%
        31.0
        PT120D2T0_GuelphTEAMR_S35_L002_R2_001
        48.5%
        51%
        31.0
        PT120D2T1_GuelphTEAMR_S40_L002_R1_001
        68.8%
        48%
        24.1
        PT120D2T1_GuelphTEAMR_S40_L002_R2_001
        64.8%
        48%
        24.1
        PT120D3T0_GuelphTEAMR_S36_L002_R1_001
        58.5%
        51%
        29.9
        PT120D3T0_GuelphTEAMR_S36_L002_R2_001
        56.4%
        51%
        29.9
        PT120D3T1_GuelphTEAMR_S41_L002_R1_001
        59.3%
        50%
        33.1
        PT120D3T1_GuelphTEAMR_S41_L002_R2_001
        56.8%
        50%
        33.1
        PT120H1T0_GuelphTEAMR_S32_L002_R1_001
        65.3%
        49%
        30.4
        PT120H1T0_GuelphTEAMR_S32_L002_R2_001
        62.7%
        49%
        30.4
        PT120H1T1_GuelphTEAMR_S37_L002_R1_001
        65.6%
        49%
        24.0
        PT120H1T1_GuelphTEAMR_S37_L002_R2_001
        63.0%
        49%
        24.0
        PT120H2T0_GuelphTEAMR_S33_L002_R1_001
        64.2%
        49%
        24.2
        PT120H2T0_GuelphTEAMR_S33_L002_R2_001
        62.5%
        49%
        24.2
        PT120H2T1_GuelphTEAMR_S38_L002_R1_001
        64.6%
        49%
        20.0
        PT120H2T1_GuelphTEAMR_S38_L002_R2_001
        62.2%
        49%
        20.0
        PT125D1T0_GuelphTEAMR_S44_L002_R1_001
        63.9%
        50%
        34.5
        PT125D1T0_GuelphTEAMR_S44_L002_R2_001
        62.2%
        50%
        34.5
        PT125D1T1_GuelphTEAMR_S47_L002_R1_001
        44.5%
        45%
        21.6
        PT125D1T1_GuelphTEAMR_S47_L002_R2_001
        43.4%
        45%
        21.6
        PT125H1T0_GuelphTEAMR_S42_L002_R1_001
        36.0%
        51%
        22.8
        PT125H1T0_GuelphTEAMR_S42_L002_R2_001
        33.6%
        51%
        22.8
        PT125H1T1_GuelphTEAMR_S45_L002_R1_001
        70.8%
        48%
        33.2
        PT125H1T1_GuelphTEAMR_S45_L002_R2_001
        68.0%
        48%
        33.2
        PT125H2T0_GuelphTEAMR_S43_L002_R1_001
        68.1%
        50%
        34.7
        PT125H2T0_GuelphTEAMR_S43_L002_R2_001
        66.6%
        50%
        34.7
        PT125H2T1_GuelphTEAMR_S46_L002_R1_001
        57.4%
        50%
        21.4
        PT125H2T1_GuelphTEAMR_S46_L002_R2_001
        55.3%
        50%
        21.4
        PT131D1T0_GuelphTEAMR_S50_L002_R1_001
        58.7%
        51%
        33.6
        PT131D1T0_GuelphTEAMR_S50_L002_R2_001
        56.4%
        51%
        33.6
        PT131D1T1_GuelphTEAMR_S53_L002_R1_001
        67.6%
        50%
        25.7
        PT131D1T1_GuelphTEAMR_S53_L002_R2_001
        64.7%
        50%
        25.7
        PT131H1T0_GuelphTEAMR_S48_L002_R1_001
        57.6%
        47%
        25.6
        PT131H1T0_GuelphTEAMR_S48_L002_R2_001
        53.5%
        47%
        25.6
        PT131H1T1_GuelphTEAMR_S51_L002_R1_001
        73.1%
        50%
        34.7
        PT131H1T1_GuelphTEAMR_S51_L002_R2_001
        72.5%
        50%
        34.7
        PT131H2T0_GuelphTEAMR_S49_L002_R1_001
        46.8%
        50%
        28.2
        PT131H2T0_GuelphTEAMR_S49_L002_R2_001
        45.0%
        50%
        28.2
        PT131H2T1_GuelphTEAMR_S52_L002_R1_001
        55.8%
        51%
        21.6
        PT131H2T1_GuelphTEAMR_S52_L002_R2_001
        54.1%
        51%
        21.6
        PT205D1T0_GuelphTEAMR_S56_L002_R1_001
        54.2%
        46%
        26.4
        PT205D1T0_GuelphTEAMR_S56_L002_R2_001
        52.8%
        46%
        26.4
        PT205D1T1_GuelphTEAMR_S59_L002_R1_001
        27.5%
        48%
        17.3
        PT205D1T1_GuelphTEAMR_S59_L002_R2_001
        25.6%
        49%
        17.3
        PT205H2T0_GuelphTEAMR_S54_L002_R1_001
        71.1%
        50%
        34.4
        PT205H2T0_GuelphTEAMR_S54_L002_R2_001
        69.0%
        50%
        34.4
        PT205H2T1_GuelphTEAMR_S57_L002_R1_001
        66.4%
        50%
        24.0
        PT205H2T1_GuelphTEAMR_S57_L002_R2_001
        63.7%
        50%
        24.0
        PT205H4T0_GuelphTEAMR_S55_L002_R1_001
        53.9%
        49%
        21.5
        PT205H4T0_GuelphTEAMR_S55_L002_R2_001
        52.2%
        49%
        21.5
        PT205H4T1_GuelphTEAMR_S58_L002_R1_001
        58.0%
        52%
        27.1
        PT205H4T1_GuelphTEAMR_S58_L002_R2_001
        56.4%
        52%
        27.1
        PT218D1T0_GuelphTEAMR_S61_L002_R1_001
        55.0%
        51%
        31.2
        PT218D1T0_GuelphTEAMR_S61_L002_R2_001
        53.2%
        51%
        31.2
        PT218D1T1_GuelphTEAMR_S63_L002_R1_001
        74.8%
        50%
        18.7
        PT218D1T1_GuelphTEAMR_S63_L002_R2_001
        71.6%
        50%
        18.7
        PT218H1T0_GuelphTEAMR_S60_L002_R1_001
        64.1%
        52%
        30.1
        PT218H1T0_GuelphTEAMR_S60_L002_R2_001
        62.0%
        52%
        30.1
        PT218H1T1_GuelphTEAMR_S62_L002_R1_001
        75.3%
        51%
        39.2
        PT218H1T1_GuelphTEAMR_S62_L002_R2_001
        74.1%
        51%
        39.2
        PT221D1T0_GuelphTEAMR_S66_L002_R1_001
        80.8%
        51%
        50.7
        PT221D1T0_GuelphTEAMR_S66_L002_R2_001
        79.5%
        51%
        50.7
        PT221D1T1_GuelphTEAMR_S69_L002_R1_001
        80.4%
        49%
        61.5
        PT221D1T1_GuelphTEAMR_S69_L002_R2_001
        78.8%
        49%
        61.5
        PT221H1T0_GuelphTEAMR_S64_L002_R1_001
        62.6%
        49%
        31.4
        PT221H1T0_GuelphTEAMR_S64_L002_R2_001
        60.8%
        49%
        31.4
        PT221H1T1_GuelphTEAMR_S67_L002_R1_001
        68.6%
        51%
        31.7
        PT221H1T1_GuelphTEAMR_S67_L002_R2_001
        66.1%
        51%
        31.7
        PT221H2T0_GuelphTEAMR_S65_L002_R1_001
        62.0%
        49%
        26.8
        PT221H2T0_GuelphTEAMR_S65_L002_R2_001
        59.8%
        49%
        26.8
        PT221H2T1_GuelphTEAMR_S68_L002_R1_001
        74.1%
        51%
        28.4
        PT221H2T1_GuelphTEAMR_S68_L002_R2_001
        73.1%
        51%
        28.4
        UK002D1T0_GuelphTEAMR_S47_L001_R1_001
        77.2%
        51%
        37.7
        UK002D1T0_GuelphTEAMR_S47_L001_R2_001
        73.2%
        51%
        37.7
        UK002H1T0_GuelphTEAMR_S45_L001_R1_001
        62.9%
        52%
        33.2
        UK002H1T0_GuelphTEAMR_S45_L001_R2_001
        58.8%
        52%
        33.2
        UK002H2T0_GuelphTEAMR_S46_L001_R1_001
        77.7%
        53%
        41.5
        UK002H2T0_GuelphTEAMR_S46_L001_R2_001
        74.3%
        53%
        41.5
        UK005D1T0_GuelphTEAMR_S50_L001_R1_001
        83.2%
        49%
        42.8
        UK005D1T0_GuelphTEAMR_S50_L001_R2_001
        79.9%
        49%
        42.8
        UK005H1T0_GuelphTEAMR_S48_L001_R1_001
        76.2%
        53%
        46.0
        UK005H1T0_GuelphTEAMR_S48_L001_R2_001
        71.8%
        53%
        46.0
        UK005H2T0_GuelphTEAMR_S49_L001_R1_001
        71.9%
        53%
        39.4
        UK005H2T0_GuelphTEAMR_S49_L001_R2_001
        67.9%
        53%
        39.4
        UK008D1T0B_GuelphTEAMR_S74_L002_R1_001
        63.8%
        49%
        30.6
        UK008D1T0B_GuelphTEAMR_S74_L002_R2_001
        61.3%
        49%
        30.6
        UK008D1T0_GuelphTEAMR_S52_L001_R1_001
        28.7%
        45%
        25.3
        UK008D1T0_GuelphTEAMR_S52_L001_R2_001
        27.0%
        45%
        25.3
        UK008H1T0_GuelphTEAMR_S51_L001_R1_001
        59.8%
        51%
        41.8
        UK008H1T0_GuelphTEAMR_S51_L001_R2_001
        56.0%
        51%
        41.8
        UK012D1T0_GuelphTEAMR_S54_L001_R1_001
        37.3%
        44%
        44.4
        UK012D1T0_GuelphTEAMR_S54_L001_R2_001
        35.1%
        44%
        44.4
        UK012H1T0_GuelphTEAMR_S53_L001_R1_001
        67.3%
        51%
        42.0
        UK012H1T0_GuelphTEAMR_S53_L001_R2_001
        62.2%
        52%
        42.0
        UK014D1T0B_GuelphTEAMR_S75_L002_R1_001
        79.5%
        48%
        33.6
        UK014D1T0B_GuelphTEAMR_S75_L002_R2_001
        76.6%
        47%
        33.6
        UK014D1T0_GuelphTEAMR_S57_L001_R1_001
        81.4%
        48%
        34.3
        UK014D1T0_GuelphTEAMR_S57_L001_R2_001
        77.0%
        48%
        34.3
        UK014H1T0_GuelphTEAMR_S55_L001_R1_001
        75.9%
        48%
        40.0
        UK014H1T0_GuelphTEAMR_S55_L001_R2_001
        71.6%
        48%
        40.0
        UK014H2T0_GuelphTEAMR_S56_L001_R1_001
        66.3%
        52%
        37.0
        UK014H2T0_GuelphTEAMR_S56_L001_R2_001
        61.6%
        52%
        37.0
        UK015D1T0_GuelphTEAMR_S60_L001_R1_001
        71.1%
        47%
        33.5
        UK015D1T0_GuelphTEAMR_S60_L001_R2_001
        67.0%
        47%
        33.5
        UK015H1T0_GuelphTEAMR_S58_L001_R1_001
        73.4%
        52%
        33.5
        UK015H1T0_GuelphTEAMR_S58_L001_R2_001
        69.5%
        52%
        33.5
        UK015H2T0_GuelphTEAMR_S59_L001_R1_001
        77.6%
        51%
        39.4
        UK015H2T0_GuelphTEAMR_S59_L001_R2_001
        73.3%
        51%
        39.4
        UK018D1T0_GuelphTEAMR_S62_L001_R1_001
        68.0%
        46%
        26.2
        UK018D1T0_GuelphTEAMR_S62_L001_R2_001
        64.3%
        46%
        26.2
        UK018H1T0_GuelphTEAMR_S61_L001_R1_001
        66.7%
        51%
        28.5
        UK018H1T0_GuelphTEAMR_S61_L001_R2_001
        62.9%
        51%
        28.5
        UK019D1T0_GuelphTEAMR_S65_L001_R1_001
        82.1%
        49%
        28.7
        UK019D1T0_GuelphTEAMR_S65_L001_R2_001
        78.2%
        49%
        28.7
        UK019H1T0_GuelphTEAMR_S63_L001_R1_001
        53.1%
        49%
        49.8
        UK019H1T0_GuelphTEAMR_S63_L001_R2_001
        48.5%
        49%
        49.8
        UK019H2T0_GuelphTEAMR_S64_L001_R1_001
        75.4%
        51%
        47.0
        UK019H2T0_GuelphTEAMR_S64_L001_R2_001
        71.9%
        51%
        47.0
        UK020D1T0_GuelphTEAMR_S67_L001_R1_001
        64.8%
        52%
        64.6
        UK020D1T0_GuelphTEAMR_S67_L001_R2_001
        59.7%
        52%
        64.6
        UK020H1T0_GuelphTEAMR_S66_L001_R1_001
        66.3%
        53%
        22.3
        UK020H1T0_GuelphTEAMR_S66_L001_R2_001
        61.9%
        53%
        22.3
        UK026D1T0_GuelphTEAMR_S1_L002_R1_001
        71.5%
        50%
        23.5
        UK026D1T0_GuelphTEAMR_S1_L002_R2_001
        69.1%
        50%
        23.5
        UK026H1T0_GuelphTEAMR_S68_L001_R1_001
        72.3%
        53%
        28.2
        UK026H1T0_GuelphTEAMR_S68_L001_R2_001
        66.9%
        53%
        28.2
        UK028D1T0_GuelphTEAMR_S3_L002_R1_001
        49.7%
        49%
        47.0
        UK028D1T0_GuelphTEAMR_S3_L002_R2_001
        49.1%
        49%
        47.0
        UK028H1T0_GuelphTEAMR_S2_L002_R1_001
        47.4%
        52%
        21.8
        UK028H1T0_GuelphTEAMR_S2_L002_R2_001
        45.9%
        52%
        21.8
        UK031D1T0_GuelphTEAMR_S5_L002_R1_001
        82.5%
        47%
        34.1
        UK031D1T0_GuelphTEAMR_S5_L002_R2_001
        80.3%
        47%
        34.1
        UK031H1T0_GuelphTEAMR_S4_L002_R1_001
        19.3%
        47%
        30.5
        UK031H1T0_GuelphTEAMR_S4_L002_R2_001
        19.0%
        47%
        30.5
        UK033D1T0_GuelphTEAMR_S7_L002_R1_001
        73.0%
        48%
        33.5
        UK033D1T0_GuelphTEAMR_S7_L002_R2_001
        71.0%
        48%
        33.5
        UK033H1T0_GuelphTEAMR_S6_L002_R1_001
        74.0%
        50%
        32.8
        UK033H1T0_GuelphTEAMR_S6_L002_R2_001
        72.0%
        50%
        32.8
        UK034D1T0_GuelphTEAMR_S9_L002_R1_001
        75.0%
        46%
        32.4
        UK034D1T0_GuelphTEAMR_S9_L002_R2_001
        72.2%
        46%
        32.4
        UK034H1T0_GuelphTEAMR_S8_L002_R1_001
        75.4%
        52%
        36.1
        UK034H1T0_GuelphTEAMR_S8_L002_R2_001
        73.0%
        52%
        36.1
        UK036D1T0B_GuelphTEAMR_S76_L002_R1_001
        71.2%
        49%
        15.3
        UK036D1T0B_GuelphTEAMR_S76_L002_R2_001
        68.1%
        49%
        15.3
        UK036D1T0_GuelphTEAMR_S11_L002_R1_001
        70.9%
        48%
        22.3
        UK036D1T0_GuelphTEAMR_S11_L002_R2_001
        67.6%
        48%
        22.3
        UK036H1T0_GuelphTEAMR_S10_L002_R1_001
        69.7%
        51%
        34.7
        UK036H1T0_GuelphTEAMR_S10_L002_R2_001
        68.8%
        51%
        34.7
        UK038D2T0_GuelphTEAMR_S13_L002_R1_001
        72.9%
        47%
        26.4
        UK038D2T0_GuelphTEAMR_S13_L002_R2_001
        70.8%
        47%
        26.4
        UK038H1T0_GuelphTEAMR_S12_L002_R1_001
        61.1%
        52%
        29.5
        UK038H1T0_GuelphTEAMR_S12_L002_R2_001
        58.6%
        52%
        29.5
        UK044D1T0_GuelphTEAMR_S15_L002_R1_001
        71.1%
        51%
        29.9
        UK044D1T0_GuelphTEAMR_S15_L002_R2_001
        68.2%
        51%
        29.9
        UK044D2T0_GuelphTEAMR_S16_L002_R1_001
        76.8%
        50%
        30.7
        UK044D2T0_GuelphTEAMR_S16_L002_R2_001
        74.2%
        50%
        30.7
        UK044D3T0_GuelphTEAMR_S17_L002_R1_001
        76.0%
        48%
        27.8
        UK044D3T0_GuelphTEAMR_S17_L002_R2_001
        73.5%
        48%
        27.8
        UK044H1T0_GuelphTEAMR_S14_L002_R1_001
        80.3%
        50%
        37.6
        UK044H1T0_GuelphTEAMR_S14_L002_R2_001
        77.6%
        50%
        37.6
        UK047D1T0B_GuelphTEAMR_S77_L002_R1_001
        75.9%
        48%
        22.8
        UK047D1T0B_GuelphTEAMR_S77_L002_R2_001
        73.5%
        48%
        22.8
        UK047D1T0_GuelphTEAMR_S19_L002_R1_001
        76.3%
        48%
        27.8
        UK047D1T0_GuelphTEAMR_S19_L002_R2_001
        74.1%
        48%
        27.8
        UK047H1T0_GuelphTEAMR_S18_L002_R1_001
        71.1%
        52%
        49.2
        UK047H1T0_GuelphTEAMR_S18_L002_R2_001
        69.8%
        52%
        49.2
        UK053D1T0_GuelphTEAMR_S21_L002_R1_001
        46.5%
        44%
        27.5
        UK053D1T0_GuelphTEAMR_S21_L002_R2_001
        44.1%
        44%
        27.5
        UK053H1T0_GuelphTEAMR_S20_L002_R1_001
        71.1%
        51%
        43.8
        UK053H1T0_GuelphTEAMR_S20_L002_R2_001
        69.3%
        51%
        43.8
        command
        0
        command.err
        0

        Snippy

        Snippy is used for rapid haploid variant calling and core genome alignment.

        Snippy Variants

        This plot shows the different variant types reported by snippy.

        Error - was not able to plot data.


        FastQC

        FastQC is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge.

        Sequence Counts

        Sequence counts for each sample. Duplicate read counts are an estimate only.

        This plot show the total number of reads, broken down into unique and duplicate if possible (only more recent versions of FastQC give duplicate info).

        You can read more about duplicate calculation in the FastQC documentation. A small part has been copied here for convenience:

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Quality Histograms

        The mean quality value across each base position in the read.

        To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

        Taken from the FastQC help:

        The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Sequence Quality Scores

        The number of reads with average quality scores. Shows if a subset of reads has poor quality.

        From the FastQC help:

        The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Base Sequence Content

        The proportion of each base position for which each of the four normal DNA bases has been called.

        To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor.

        To see the data as a line plot, as in the original FastQC graph, click on a sample track.

        From the FastQC help:

        Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.

        In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.

        It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.

        Click a sample row to see a line plot for that dataset.
        Rollover for sample name
        Position: -
        %T: -
        %C: -
        %A: -
        %G: -

        Per Sequence GC Content

        The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.

        From the FastQC help:

        This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content.

        In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution.

        An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Base N Content

        The percentage of base calls at each position for which an N was called.

        From the FastQC help:

        If a sequencer is unable to make a base call with sufficient confidence then it will normally substitute an N rather than a conventional base call. This graph shows the percentage of base calls at each position for which an N was called.

        It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Length Distribution

        All samples have sequences of a single length (151bp).

        Sequence Duplication Levels

        The relative level of duplication found for every sequence.

        From the FastQC Help:

        In a diverse library most sequences will occur only once in the final set. A low level of duplication may indicate a very high level of coverage of the target sequence, but a high level of duplication is more likely to indicate some kind of enrichment bias (eg PCR over amplification). This graph shows the degree of duplication for every sequence in a library: the relative number of sequences with different degrees of duplication.

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        In a properly diverse library most sequences should fall into the far left of the plot in both the red and blue lines. A general level of enrichment, indicating broad oversequencing in the library will tend to flatten the lines, lowering the low end and generally raising other categories. More specific enrichments of subsets, or the presence of low complexity contaminants will tend to produce spikes towards the right of the plot.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Overrepresented sequences

        The total amount of overrepresented sequences found in each library.

        FastQC calculates and lists overrepresented sequences in FastQ files. It would not be possible to show this for all samples in a MultiQC report, so instead this plot shows the number of sequences categorized as over represented.

        Sometimes, a single sequence may account for a large number of reads in a dataset. To show this, the bars are split into two: the first shows the overrepresented reads that come from the single most common sequence. The second shows the total count from all remaining overrepresented sequences.

        From the FastQC Help:

        A normal high-throughput library will contain a diverse set of sequences, with no individual sequence making up a tiny fraction of the whole. Finding that a single sequence is very overrepresented in the set either means that it is highly biologically significant, or indicates that the library is contaminated, or not as diverse as you expected.

        FastQC lists all of the sequences which make up more than 0.1% of the total. To conserve memory only sequences which appear in the first 100,000 sequences are tracked to the end of the file. It is therefore possible that a sequence which is overrepresented but doesn't appear at the start of the file for some reason could be missed by this module.

        290 samples had less than 1% of reads made up of overrepresented sequences

        Adapter Content

        The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.

        Note that only samples with ≥ 0.1% adapter contamination are shown.

        There may be several lines per sample, as one is shown for each adapter detected in the file.

        From the FastQC Help:

        The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Status Checks

        Status for each FastQC section showing whether results seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        FastQC assigns a status for each section of the report. These give a quick evaluation of whether the results of the analysis seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        It is important to stress that although the analysis results appear to give a pass/fail result, these evaluations must be taken in the context of what you expect from your library. A 'normal' sample as far as FastQC is concerned is random and diverse. Some experiments may be expected to produce libraries which are biased in particular ways. You should treat the summary evaluations therefore as pointers to where you should concentrate your attention and understand why your library may not look random and diverse.

        Specific guidance on how to interpret the output of each module can be found in the relevant report section, or in the FastQC help.

        In this heatmap, we summarise all of these into a single heatmap for a quick overview. Note that not all FastQC sections have plots in MultiQC reports, but all status checks are shown in this heatmap.

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